PCSC framework will stay in Mac OS X 10.11 El Capitan

I learned that this will not the be case. It was a misinterpretation on my side.

PCSC framework

On the page "OS X v.10.11 API Diffs" PCSC is removed in the 'Modules' section but is not removed in the 'Framework' section. The PCSC framework is still provided and supported in El Capitan.

This means that PCSC.framework public API will not changed at all and is perfectly usable from C/C++/ObjC applications.

Swift

For developing smart card applications with Swift, CryptoTokenKit framework/module is recommended by Apple.

The effect that PCSC Module is removed is that it will not be possible to import PCSC in a Swift application on El Capitan.

On Yosemite you can import PCSC but no SCard functions nor declarations are actually visible and nothing could be used, the import is in fact broken. So using El Capitan should not break existing Swift application.